Jian Lu, Ph.D.
Research group of evolution and population genomics
Professor, College of Life Sciences, Peking University
tel：
E-mail：luj@pku.edu.cn
1.Non-coding RNA origin, evolution, and the new mechanism of non-coding RNA gene evolution drivers
2.The use of the target gene RNA-Seq, ribosome profiling, gene knockout and evolutionary genomics and other methods to identify non-coding RNA regulation
3.Functional genomics study on regulation of transcription.
The function and evolution of miRNAs. MicroRNA (miRNA) participate in many processes and has very important biological functions in organisms. It regulates the expression of the target genes through degradation of transcripts or/and translation repression. As its complexity and important roles, microRNA regulation has become one of the research hotspots in life sciences. Our study material included hundreds of miRNA mutant strains of Drosophila. We used RNA-seq and ribosome-profiling to find out the target genes of miRNAs in the transcriptional and translational levels. The effects of mutation on miRNAs and target genes on the miRNA:mRNA paring are also our research focus. By comparing miRNA expression in different stages of development and under stresses, we could uncover the roles of miRNAs in transcriptome and translatome stabilization.
Co-evolution between transposable element and piRNAs. Transposable element (TE) is an important type of selfish genetic elements and it lowers the fitness of the host. In Drosophila melanogaster, the host develops small non-coding RNA (siRNA and piRNA) to suppress TE, and piRNAs in the germline is especially important in TE suppression. Our hypothesis is that piRNA and TE are co-evolved: when a TE invades the genome, the responding suppressing piRNA is soon produced. We investigated TE composition, insertion sites and frequency in the 92 strains of D.melanogaster which have been sequenced. We have found TE insertions are population-specific. We also sequenced small RNAs from 10 different strains of D.melanogaster and uncovered the co-evolution between piRNAs and TE. Our results showed that most of the active TE had corresponding piRNAs, and they were positively related. The production of piRNAs was also related to sex, recombination rate and chromosome modification state.
Wu XK, Xu MZ, Yang JR, Lu J. (2024) Genome-wide impact of codon usage bias on translation optimization in Drosophila melanogaster. Nat. Commun., 15: 8329.
Chen JH, Liu CL, Li WX, Zhang WX, Wang YR, Clark AG, Lu J. (2024) From sub-saharan africa to China: evolutionary history and adaptation of Drosophila melanogaster revealed by population genomics.Sci. Adv., 10: eadh3425.
Yao ZC, Zhang L, Duan YE, Tang XL, Lu J. (2024) Molecular insights into the adaptive evolution of SARS-CoV-2 spike protein. J. Infect., 88: 106121.
Wu CC, Ruhan A, Ye S, Ye F, Huo WB, Lu RJ, Tang Y, Yang JW, Meng XH, Tang Y, Chen S, Zhao L, Huang BY, Zhang ZX, Chen YD, Li DF, Wang WL, Shan KJ, Lu J, Tan WJ. (2024) Rapid identification of full-length genome and tracing variations of monkeypox virus in clinical specimens based on mNGS and amplicon sequencing. Virol. Sin., 39: 134-143.
Wang YR, Tang XL, Lu J.(2024) Convergent and pergent evolution of microRNA-mediated regulation in metazoans. Biol. Rev., 99: 525-545.
Shan KJ, Wu CC, Tang XL, Lu RJ, Hu YL, Tan WJ, Lu J. (2024) Molecular evolution of protein sequences and codon usage in monkeypox viruses. Genom. Proteom. Bioinform., 22: qzad003.
Jin KC, Tang XL, Qian ZH, Wu ZQ, Yang ZF, Qian T, Hon C, Lu J. (2024) Modeling viral evolution: A novel SIRSVIDE framework with application to SARS-CoV-2 dynamics. hLife, 2: 227-245.
Wu XK, Shan KJ, Zan FW, Tang XL, Qian ZH, Lu J. (2023) Optimization and deoptimization of codons in SARS-CoV-2 and related implications for vaccine development. Adv. Sci., 10: e2205445.
Tang XL, Qian ZH, Lu XM, Lu J. (2023) Adaptive evolution of the spike protein in coronaviruses. Mol. Biol. Evol., 40: msad089.
Ou XY, Xu G, Li P, Liu Y, Zan FW, Liu P, Hu JX, Lu X, Dong SW, Zhou Y, Mu ZX, Wu ZQ, Wang JW, Jin Q, Liu PH, Lu J, Wang XX, Qian ZH. (2023) Host susceptibility and structural and immunological insight of S proteins of two SARS-CoV-2 closely related bat coronaviruses. Cell Discov., 9: 78.
Li P, Hu JX, Liu Y#, Ou XY, Mu ZX, Lu X, Zan FW, Cao MM, Tan L, Dong SW, Zhou Y, Lu J, Jin Q, Wang JW, Wu ZQ, Zhang YT, Qian ZH (2023) Effect of polymorphism in Rhinolophus affinis ACE2 on entry of SARS-CoV-2 related bat coronaviruses. PLoS Pathog., 19: e1011116.
Hu SX, Wu CL, Wu XK, Ma XH, Shu C, Chen Q, Zheng AQ, Yang HT, Lu J, Du P, Gao GF, Wang QH. (2023) Classification of five SARS-CoV-2 serotypes based on RBD antigenicities. Sci. Bull., 68: 3003-3012.
Duan YG, Tang XL, Lu J. (2022) Evolutionary driving forces of A-to-I editing in metazoans. Wiley Interdiscip. Rev.-RNA, 13: e1666.
Ruan YS, Hou M, Tang XL, He XL, Lu XM, Lu J, Wu CI, Wen HJ. (2022) The runaway evolution of SARS-CoV-2 leading to the highly evolved delta strain. Mol. Biol. Evol., 39: msac046.
Sun Q, Shu C, Shi W, Luo Y, Fan G, Nie J, Bi Y, Wang Q, Qi J, Lu J, Zhou Y, Shen Z, Meng Z, Zhang X, Yu Z, Gao S, Wu L, Ma J, Hu S. (2022) VarEPS: an evaluation and prewarning system of known and virtual variations of SARS-CoV-2 genomes. Nucl. Acids Res., 50: D888-D897.
Qian ZH, Li P, Tang XL, Lu J. (2022) Evolutionary dynamics of the severe acute respiratory syndrome coronavirus 2 genomes. Med. Rev., 2: 3-22.
Hu B, Liu R, Tang XL, Pan YC, Wang M, Tong YQ, Ye GM, Shen GG, Ying RC, Fu AS, Li D, Zhao WX, Peng J, Guo J, Men D, Yao XM, Wang YR, Zhang H, Feng ZH, Yu JP, Chen LJ, Deng ZX, Lu XM, Zhang YP, Li YR, Liu BD, Yu LL, Li Y, Lu J, Liu TG. (2021) The concordance between the evolutionary trend and the clinical manifestation of the two SARS-CoV-2 variants. Natl. Sci. Rev., 8: nwab073.
Ruan YS, Luo ZD, Tang XL, Li GH, Wen HJ, He XL, Lu XM, Lu J, Wu CI. (2021) On the founder effect in COVID-19 outbreaks: how many infected travelers may have started them all? Natl. Sci. Rev., 8: nwaa246.
Yu TX, Huang X, Dou SQ, Tang XL, Luo SQ, Theurkauf WE, Lu J, Weng ZP. (2021) A benchmark and an algorithm for detecting germline transposon insertions and measuring de novo transposon insertion frequencies. Nucleic Acids Res., 49: e44.
Zhang H, Wang YR, Wu XK, Tang XL, Wu CC, Lu J. (2021) Determinants of genome-wide distribution and evolution of uORFs in eukaryotes. Nat. Commun., 12: 1076.
Tang XL, Ying RC, Yao XM, Li GH, Wu CC, Tang YYL, Li ZD, Kuang BS, Wu F, Chi CS, Du XM, Qin Y, Gao SH, Hu SNA, Ma JC, Liu TG, Pang XH, Wang JW, Zhao GP, Tan WJ, Zhang YP, Lu XM, Lu J. (2021) Evolutionary analysis and lineage designation of SARS-CoV-2 genomes. Sci. Bull., 66: 2297-2311.
Zhang H, Wang YR, Tang XL, Dou SQ, Sun YQ, Zhang Q, Lu J. (2021) Combinatorial regulation of gene expression by uORFs and microRNAs in Drosophila. Sci. Bull., 66: 225-228.
Duan YG, Tang XL, Lu J. (2021) Evolutionary driving forces of A-to-I editing in metazoans. Wiley Interdiscip. Rev.-RNA, e1666.
Duan YG, Dou SQ, Porath HT, Huang JX, Eisenberg E, Lu J. (2021) A-to-I RNA editing in honeybees shows signals of adaptation and convergent evolution. iScience, 24: 101983.
Peng MS, Li JB, Cai ZF, Liu H, Tang X, Ying R, Zhang JN, Tao JJ, Yin TT, Zhang T, Hu JY, Wu RN, Zhou ZY, Zhang ZG, Yu L, Yao YG, Shi ZL, Lu XM, Lu J, Zhang YP. (2021) The high persity of SARS-CoV-2-related coronaviruses in pangolins alerts potential ecological risks. Zool. Res., 42: 834-844.
Wu Z, Jin Q, Wu G, Lu J, Li M, Guo D, Lan K, Feng L, Qian Z, Ren L, Tan W, Xu W, Yang W, Wang J, Wang C.(2021)SARS-CoV-2's origin should be investigated worldwide for pandemic prevention. Lancet., 398: 1299-1303.
Feng YQ, Xu HZ, Liu JH, Xie N, Gao L, He YY, Yao Y, Lv FX, Zhang Y, Lu J, Zhang W, Li CY, Hu XL, Yang ZH, Xiao RP. (2021) Functional and adaptive significance of promoter mutations that affect pergent myocardial expressions ofTRIM72in primates. Mol. Biol. Evol., 38: 2930-2945.
Wu CI, Wen H, Lu J, Su XD, Hughes AC, Zhai W, Chen C, Chen H, Li M, Song S, Qian Z, Wang Q, Chen B, Guo Z, Ruan Y, Lu X, Wei F, Jin L, Kang L, Xue Y, Zhao G, Zhang YP. (2021) On the origin of SARS-CoV-2-The blind watchmaker argument. Sci. China-Life Sci., 64: 1560-1563.
Tang XL, Wu CC, Li X, Song YH, Yao XM, Wu XK, Duan YG, Zhang H, Wang YR, Qian ZH, Cui J, Lu J. (2020) On the origin and continuing evolution of SARS-CoV-2. Natl. Sci. Rev., 7: 1012-1023.
Wang Y, Zhang H, Lu J. (2020) Recent advances in ribosome profiling for deciphering translational regulation. Methods., 176:46-54.
Li T, Tang XL, Wu CC, Yao XM, Wang YR, Lu XM, Lu J. (2020) The use of SARS-CoV-2-related coronaviruses from bats and pangolins to polarize mutations in SARS-Cov-2. Sci. China Life Sci., 63: 1608-1611.
Luo SQ, Zhang H, Duan YG, Yao XM, Clark AG, Lu J. (2020) The evolutionary arms race between transposable elements and piRNAs in Drosophila melanogaster. BMC Evol. Biol., 20: 14.
Zhijuan Wang, Junhao Chen, Xiaolu Tang, Kejia Shan, Xinmin Yao, Xinyue Chen, Ruochen Ying, Chenlu Liu, Weixuan Li, Hairong Wang, Peixiang Gao, Dake Gao, Kaichun Jin, Qiheng Xu, Xinning Dong, Lin Zhang, Mengze Xu
